rs2241109

Variant names:

• chr1-156203291-C-T
• rs2241109
• NM_014655.4:c.625+2819C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014655.4(SLC25A44):​c.625+2819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,126 control chromosomes in the GnomAD database, including 4,064 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4064 hom., cov: 32)
• Consequence: SLC25A44 NM_014655.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 16 publications found

Genes affected

SLC25A44 (HGNC:29036): (solute carrier family 25 member 44) SLC25A44 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014655.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A44	NM_014655.4	MANE Select	c.625+2819C>T		intron	N/A	NP_055470.1
	SLC25A44	NM_001286184.2		c.625+2819C>T		intron	N/A	NP_001273113.1
	SLC25A44	NM_001377385.1		c.625+2819C>T		intron	N/A	NP_001364314.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A44	ENST00000359511.5	TSL:1 MANE Select	c.625+2819C>T		intron	N/A	ENSP00000352497.4
	SLC25A44	ENST00000423538.6	TSL:1	c.625+2819C>T		intron	N/A	ENSP00000407560.3
	SLC25A44	ENST00000469537.1	TSL:1	n.4268+2819C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33004 AN: 152008 Hom.: 4063 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.227

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.217 AC: 33017 AN: 152126 Hom.: 4064 Cov.: 32 AF XY: 0.215 AC XY: 15997 AN XY: 74362

African (AFR) AF: 0.140 AC: 5803 AN: 41502

American (AMR) AF: 0.191 AC: 2918 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3468

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5184

South Asian (SAS) AF: 0.157 AC: 756 AN: 4824

European-Finnish (FIN) AF: 0.299 AC: 3152 AN: 10548

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18745 AN: 67988

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.253 Hom.: 17605

Bravo AF: 0.205

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2241109; hg19: chr1-156173082;